RT-PCR and nested RT-PCR for detection and genotyping of group A rotavirus from faecal samples of dairy cattle farms from Southern Karnataka

Rotavirusesare significant causes of severe diarrhoea in both humans and animals resulting in significant economic losses on local as well as global scale.The present study was carried out to determine the prevalence and characterization of group A rotavirus in cattle faeces.A total of 106 cattle faecal sample from four districts of Karnataka were subjected to RNA extraction, and cDNA was synthesized and subjected to RT-PCR by targeting the VP6 gene, in which 9 samples yielded an expected amplicon of 309 bp, giving an overall prevalence of 8.49%.Upon G and P genotyping, all 9 samples in the first round of RT-PCR yielded an expected PCR product of 1062 bp (VP7 gene) and 7 samples of 876 bp product for (VP4 gene).Further, second round nested RT-PCR revealed the presence of G6 (22.22%),G8 (11.11%),G9 (22.22%),P[4](11.11%),P[6](11.11%), and P[10](11.11%)genotypes.Higher prevalence was recorded in calves of less than 3 months of age (17.65%), followed by calves between 3 to 6 months of age (10.53%).Sex-wise prevalence, 7 females (77.78%) and 1 male (22.22%) were positive for group A rotavirus.The findings of this study showed the presence of common genotypes among cattle G6, G8, P[6]and uncommon genotypes G9, P[4] and P[10].This will help for further surveillance and epidemiological research on rotavirus infection and related risk factors in cattle.